Two bugfixes to parsing of GAMESS COSMO files.

[thomvet]

This introduces two bugfixes for the parsing of GAMESS output files:

1. Previous regular expression only matched segments and atoms after the first minus sign appeared in the coordinate list. This is the case in the example file the script was tested against, but of course is not a general occurrence... (the molecule may be anywhere in the XYZ coordinates...).

2. GAMESS puts two letter atoms in all caps in the output file ("CL" for chlorine; chlorobenzene example below) which did not match with the covalent_radius dictionary. This is at least the case in the July 2024 release (most current).

      ***** EQUILIBRIUM GEOMETRY LOCATED *****
 COORDINATES OF ALL ATOMS ARE (ANGS)
   ATOM   CHARGE       X              Y              Z
 ------------------------------------------------------------
 CL         17.0  -2.6766712684   0.0000241120  -0.0001662742
 C           6.0  -0.9172854545   0.0000161276   0.0000595843
 C           6.0  -0.2471426954   1.2054189392  -0.0000210845
 C           6.0  -0.2471613191  -1.2053999849  -0.0000242800
 C           6.0   1.1371638312   1.1977117151   0.0000227093
 C           6.0   1.1371432182  -1.1977117948   0.0000195734
 C           6.0   1.8306573054  -0.0000048068   0.0000228211
 H           1.0  -0.7895846254   2.1308893153   0.0000039874
 H           1.0  -0.7896230760  -2.1308588008  -0.0000907079
 H           1.0   1.6689625901   2.1309092192  -0.0000188121
 H           1.0   1.6689353268  -2.1309132022  -0.0000797139
 H           1.0   2.9046737930  -0.0000320009   0.0000519258 

[ianhbell]

Can you provide a test file ? It would be nice to have tests run on every commit (more a comment for me than anything)

[thomvet]

Yes, I will try to make one that has both features (Cl atom and only positive XYZ coordinates). Do you want to have it in https://github.com/usnistgov/COSMOSAC/tree/master/profiles/GAMESS_TEST ?

Edit: will also include expected output file.

[ibell]

Yes, that seems like a good location for the files